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- PDB-8ei5: Crystal structure of the WWP2 HECT domain in complex with H301, a... -

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Basic information

Entry
Database: PDB / ID: 8ei5
TitleCrystal structure of the WWP2 HECT domain in complex with H301, a Helicon Polypeptide
Components
  • H301
  • NEDD4-like E3 ubiquitin-protein ligase WWP2
KeywordsLIGASE / E3 ligase / complex / stapled peptide
Function / homology
Function and homology information


negative regulation of transporter activity / negative regulation of protein transport / extracellular transport / regulation of potassium ion transmembrane transporter activity / regulation of monoatomic ion transmembrane transport / HECT-type E3 ubiquitin transferase / transcription factor binding / RHOJ GTPase cycle / RHOQ GTPase cycle / RHOU GTPase cycle ...negative regulation of transporter activity / negative regulation of protein transport / extracellular transport / regulation of potassium ion transmembrane transporter activity / regulation of monoatomic ion transmembrane transport / HECT-type E3 ubiquitin transferase / transcription factor binding / RHOJ GTPase cycle / RHOQ GTPase cycle / RHOU GTPase cycle / protein K63-linked ubiquitination / negative regulation of Notch signaling pathway / ubiquitin ligase complex / protein autoubiquitination / regulation of membrane potential / negative regulation of DNA-binding transcription factor activity / NOTCH3 Activation and Transmission of Signal to the Nucleus / protein modification process / Regulation of PTEN stability and activity / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / RNA polymerase II-specific DNA-binding transcription factor binding / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / protein ubiquitination / symbiont entry into host cell / negative regulation of gene expression / negative regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
E3 ubiquitin-protein ligase, SMURF1 type / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Protein kinase C conserved region 2 (CalB) / WW domain / WW/rsp5/WWP domain signature. ...E3 ubiquitin-protein ligase, SMURF1 type / : / HECT domain / HECT, E3 ligase catalytic domain / HECT-domain (ubiquitin-transferase) / HECT domain profile. / Domain Homologous to E6-AP Carboxyl Terminus with / Protein kinase C conserved region 2 (CalB) / WW domain / WW/rsp5/WWP domain signature. / C2 domain / C2 domain profile. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / C2 domain superfamily
Similarity search - Domain/homology
N,N'-(1,4-phenylene)diacetamide / NEDD4-like E3 ubiquitin-protein ligase WWP2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLi, K. / Tokareva, O.S. / Thomson, T.M. / Verdine, G.L. / McGee, J.H.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Nat Commun / Year: 2023
Title: Recognition and reprogramming of E3 ubiquitin ligase surfaces by alpha-helical peptides.
Authors: Tokareva, O.S. / Li, K. / Travaline, T.L. / Thomson, T.M. / Swiecicki, J.M. / Moussa, M. / Ramirez, J.D. / Litchman, S. / Verdine, G.L. / McGee, J.H.
History
DepositionSep 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEDD4-like E3 ubiquitin-protein ligase WWP2
B: NEDD4-like E3 ubiquitin-protein ligase WWP2
C: NEDD4-like E3 ubiquitin-protein ligase WWP2
D: NEDD4-like E3 ubiquitin-protein ligase WWP2
E: H301
F: H301
G: H301
H: H301
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,78538
Polymers187,2398
Non-polymers2,54630
Water5,747319
1
A: NEDD4-like E3 ubiquitin-protein ligase WWP2
E: H301
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,77814
Polymers46,8102
Non-polymers96812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-40 kcal/mol
Surface area19900 Å2
MethodPISA
2
B: NEDD4-like E3 ubiquitin-protein ligase WWP2
F: H301
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4389
Polymers46,8102
Non-polymers6287
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-39 kcal/mol
Surface area19810 Å2
MethodPISA
3
C: NEDD4-like E3 ubiquitin-protein ligase WWP2
G: H301
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2537
Polymers46,8102
Non-polymers4445
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-44 kcal/mol
Surface area19260 Å2
MethodPISA
4
D: NEDD4-like E3 ubiquitin-protein ligase WWP2
H: H301
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3168
Polymers46,8102
Non-polymers5066
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-39 kcal/mol
Surface area19550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.660, 63.100, 122.260
Angle α, β, γ (deg.)90.000, 96.780, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 493 through 500 or resid 502...
21(chain B and (resid 493 through 500 or resid 502...
31(chain C and (resid 493 through 500 or resid 502...
41(chain D and (resid 493 through 500 or resid 502...
12(chain E and (resid 7 through 17 or resid 103))
22(chain F and (resid 7 through 17 or resid 103))
32chain G
42chain H

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 493 through 500 or resid 502...A493 - 500
121(chain A and (resid 493 through 500 or resid 502...A502 - 599
131(chain A and (resid 493 through 500 or resid 502...A601 - 605
141(chain A and (resid 493 through 500 or resid 502...A607 - 672
151(chain A and (resid 493 through 500 or resid 502...A674
161(chain A and (resid 493 through 500 or resid 502...A772 - 805
171(chain A and (resid 493 through 500 or resid 502...A808 - 818
181(chain A and (resid 493 through 500 or resid 502...A820 - 868
191(chain A and (resid 493 through 500 or resid 502...A820 - 865
211(chain B and (resid 493 through 500 or resid 502...B493 - 500
221(chain B and (resid 493 through 500 or resid 502...B502 - 599
231(chain B and (resid 493 through 500 or resid 502...B601 - 605
241(chain B and (resid 493 through 500 or resid 502...B607 - 672
251(chain B and (resid 493 through 500 or resid 502...B674
261(chain B and (resid 493 through 500 or resid 502...B676 - 699
271(chain B and (resid 493 through 500 or resid 502...B701 - 770
281(chain B and (resid 493 through 500 or resid 502...B772 - 805
291(chain B and (resid 493 through 500 or resid 502...B808 - 818
2101(chain B and (resid 493 through 500 or resid 502...B820 - 865
311(chain C and (resid 493 through 500 or resid 502...C493 - 500
321(chain C and (resid 493 through 500 or resid 502...C502 - 599
331(chain C and (resid 493 through 500 or resid 502...C601 - 605
341(chain C and (resid 493 through 500 or resid 502...C607 - 672
351(chain C and (resid 493 through 500 or resid 502...C7
361(chain C and (resid 493 through 500 or resid 502...C701 - 770
371(chain C and (resid 493 through 500 or resid 502...C772 - 805
381(chain C and (resid 493 through 500 or resid 502...C808 - 818
391(chain C and (resid 493 through 500 or resid 502...C820 - 865
411(chain D and (resid 493 through 500 or resid 502...D493 - 500
421(chain D and (resid 493 through 500 or resid 502...D502 - 599
431(chain D and (resid 493 through 500 or resid 502...D601 - 605
441(chain D and (resid 493 through 500 or resid 502...D607 - 672
451(chain D and (resid 493 through 500 or resid 502...D674
461(chain D and (resid 493 through 500 or resid 502...D676 - 699
471(chain D and (resid 493 through 500 or resid 502...D493 - 865
481(chain D and (resid 493 through 500 or resid 502...D772 - 805
491(chain D and (resid 493 through 500 or resid 502...D820 - 868
4101(chain D and (resid 493 through 500 or resid 502...D820 - 865
112(chain E and (resid 7 through 17 or resid 103))E0
212(chain F and (resid 7 through 17 or resid 103))F0
312chain GG7 - 17
412chain HH7 - 17

NCS ensembles :
ID
1
2

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGH

#1: Protein
NEDD4-like E3 ubiquitin-protein ligase WWP2 / Atrophin-1-interacting protein 2 / AIP2 / HECT-type E3 ubiquitin transferase WWP2 / WW domain- ...Atrophin-1-interacting protein 2 / AIP2 / HECT-type E3 ubiquitin transferase WWP2 / WW domain-containing protein 2


Mass: 44925.391 Da / Num. of mol.: 4 / Fragment: HECT domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WWP2 / Production host: Escherichia coli (E. coli)
References: UniProt: O00308, HECT-type E3 ubiquitin transferase
#2: Protein/peptide
H301


Mass: 1884.235 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 349 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-WHL / N,N'-(1,4-phenylene)diacetamide


Mass: 192.214 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H12N2O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M Sodium acetate, 0.1M sodium citrate pH6.0, 10% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.6→45.4 Å / Num. obs: 56697 / % possible obs: 99.9 % / Redundancy: 5.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.139 / Net I/σ(I): 7.6
Reflection shellResolution: 2.6→2.68 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4596 / CC1/2: 0.827 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Y07

4y07


Resolution: 2.6→45.4 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.262 2658 4.75 %
Rwork0.2132 53357 -
obs0.2155 56015 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.98 Å2 / Biso mean: 39.6568 Å2 / Biso min: 12.25 Å2
Refinement stepCycle: final / Resolution: 2.6→45.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12944 0 158 319 13421
Biso mean--51.4 34.75 -
Num. residues----1542
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7271X-RAY DIFFRACTION17.237TORSIONAL
12B7271X-RAY DIFFRACTION17.237TORSIONAL
13C7271X-RAY DIFFRACTION17.237TORSIONAL
14D7271X-RAY DIFFRACTION17.237TORSIONAL
21E178X-RAY DIFFRACTION17.237TORSIONAL
22F178X-RAY DIFFRACTION17.237TORSIONAL
23G178X-RAY DIFFRACTION17.237TORSIONAL
24H178X-RAY DIFFRACTION17.237TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.650.30681490.27552788293799
2.65-2.70.29961100.26642800291099
2.7-2.750.33241350.26962819295499
2.75-2.810.3351330.260527982931100
2.81-2.880.29191430.24962833297699
2.88-2.950.30211370.24752777291499
2.95-3.030.32911330.24272837297099
3.03-3.120.3121360.24152798293499
3.12-3.220.26671470.23662759290699
3.22-3.340.32081500.2252789293999
3.34-3.470.26331480.21412784293299
3.47-3.630.23841410.20182817295899
3.63-3.820.26171530.19072809296299
3.82-4.060.25591410.18762808294999
4.06-4.370.19151270.1812832295998
4.37-4.810.22111670.17442774294198
4.81-5.50.22371640.18422837300199
5.5-6.930.28761250.22942869299499
6.93-45.40.20511190.19352829294894

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